pca_scores_plot: PCA scores plot

In computational-metabolomics/structToolbox: Data processing & analysis tools for Metabolomics and other omics

PCA scores plot

Description

Plots a 2d scatter plot of the selected components

Usage

pca_scores_plot(
  xcol = "PC1",
  ycol = "PC2",
  points_to_label = "none",
  factor_name,
  ellipse = "all",
  ellipse_type = "norm",
  ellipse_confidence = 0.95,
  label_filter = character(0),
  label_factor = "rownames",
  label_size = 3.88,
  components = NULL,
  ...
)

Arguments

xcol	(numeric, integer, character) The column name, or index, of data to plot on the x-axis. The default is "PC1".
ycol	(numeric, integer, character) The column name, or index, of data to plot on the y-axis. The default is "PC2".
points_to_label	(character) Points to label. Allowed values are limited to the following: "none": No samples labels are displayed. "all": The labels for all samples are displayed. "outliers": Labels for for potential outlier samples are displayed. The default is "none".
factor_name	(character) The name of a sample-meta column to use.
ellipse	(character) Plot ellipses. Allowed values are limited to the following: "all": Ellipses are plotted for all groups and all samples. "group": Ellipses are plotted for all groups. "none": Ellipses are not included on the plot. "sample": An ellipse is plotted for all samples (ignoring group). The default is "all".
ellipse_type	(character) Type of ellipse. Allowed values are limited to the following: "norm": Multivariate normal (p = 0.95). "t": Multivariate t (p = 0.95). The default is "norm".
ellipse_confidence	(numeric) The confidence level for plotting ellipses. The default is 0.95.
label_filter	(character) Labels are only plotted for the named groups. If zero-length then all groups are included. The default is character(0).
label_factor	(character) The column name of sample_meta to use for labelling samples on the plot. "rownames" will use the row names from sample_meta. The default is "rownames".
label_size	(numeric) The text size of labels. Note this is not in Font Units. The default is 3.88.
components	(numeric, integer, NULL) The principal components used to generate the plot. If provided this parameter overrides xcol and ycol params. The default is NULL.
...	Additional slots and values passed to struct_class.

Value

A pca_scores_plot object. This object has no output slots. See chart_plot in the struct package to plot this chart object.

Inheritance

A pca_scores_plot object inherits the following struct classes:

⁠[pca_scores_plot]⁠ >> ⁠[scatter_chart]⁠ >> ⁠[chart]⁠ >> ⁠[struct_class]⁠

Examples

M = pca_scores_plot(
      components = NULL,
      xcol = 1,
      ycol = 2,
      points_to_label = "none",
      factor_name = "V1",
      ellipse = "all",
      label_filter = character(0),
      label_factor = "rownames",
      label_size = 3.88,
      ellipse_type = "norm",
      ellipse_confidence = 0.95)

D = iris_DatasetExperiment()
M = mean_centre() + PCA()
M = model_apply(M,D)
C = pca_scores_plot(factor_name = 'Species')
chart_plot(C,M[2])

computational-metabolomics/structToolbox documentation built on Feb. 12, 2024, 2:15 a.m.